X-103323975-T-G

Position:

• chrX-103323975-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.67 (18708 hom., 21540 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.670 AC: 73960 AN: 110382 Hom.: 18704 Cov.: 22 AF XY: 0.659 AC XY: 21479 AN XY: 32618

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.670 AC: 74015 AN: 110439 Hom.: 18708 Cov.: 22 AF XY: 0.659 AC XY: 21540 AN XY: 32683

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.645

Alfa AF: 0.478 Hom.: 2661

Bravo AF: 0.691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5987515; hg19: chrX-102578903;